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- PDB-2vwe: Crystal Structure of Vascular Endothelial Growth Factor-B in Comp... -

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Basic information

Entry
Database: PDB / ID: 2vwe
TitleCrystal Structure of Vascular Endothelial Growth Factor-B in Complex with a Neutralizing Antibody Fab Fragment
Components
  • (ANTI-VEGF-B MONOCLONAL ANTIBODY) x 2
  • VASCULAR ENDOTHELIAL GROWTH FACTOR B
KeywordsIMMUNE SYSTEM / GLYCOPROTEIN / CYSTEINE-KNOT / GROWTH FACTOR / VEGF-B / MITOGEN / SECRETED / ANGIOGENESIS / NEUTRALIZING ANTIBODY / HEPARIN-BINDING
Function / homology
Function and homology information


positive regulation of vascular wound healing / vascular endothelial growth factor receptor 1 binding / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / VEGF binds to VEGFR leading to receptor dimerization / induction of positive chemotaxis / protein O-linked glycosylation / coronary vasculature development / positive regulation of vascular endothelial growth factor receptor signaling pathway ...positive regulation of vascular wound healing / vascular endothelial growth factor receptor 1 binding / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / VEGF binds to VEGFR leading to receptor dimerization / induction of positive chemotaxis / protein O-linked glycosylation / coronary vasculature development / positive regulation of vascular endothelial growth factor receptor signaling pathway / sprouting angiogenesis / vascular endothelial growth factor signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / chemoattractant activity / positive regulation of cell division / vascular endothelial growth factor receptor signaling pathway / cardiac muscle contraction / positive regulation of endothelial cell proliferation / platelet alpha granule lumen / growth factor activity / Platelet degranulation / heparin binding / negative regulation of neuron apoptotic process / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / negative regulation of gene expression / positive regulation of cell population proliferation / negative regulation of apoptotic process / extracellular space / extracellular region / identical protein binding / membrane
Similarity search - Function
: / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain / Platelet-derived growth factor (PDGF) family signature. / Platelet-derived growth factor (PDGF) family profile. / Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine ...: / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain / Platelet-derived growth factor (PDGF) family signature. / Platelet-derived growth factor (PDGF) family profile. / Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Vascular endothelial growth factor B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsLeonard, P. / Scotney, P.D. / Jabeen, T. / Iyer, S. / Fabri, L.J. / Nash, A.D. / Acharya, K.R.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal Structure of Vascular Endothelial Growth Factor-B in Complex with a Neutralising Antibody Fab Fragment.
Authors: Leonard, P. / Scotney, P.D. / Jabeen, T. / Iyer, S. / Fabri, L.J. / Nash, A.D. / Acharya, K.R.
History
DepositionJun 23, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VASCULAR ENDOTHELIAL GROWTH FACTOR B
B: VASCULAR ENDOTHELIAL GROWTH FACTOR B
C: ANTI-VEGF-B MONOCLONAL ANTIBODY
E: ANTI-VEGF-B MONOCLONAL ANTIBODY
J: ANTI-VEGF-B MONOCLONAL ANTIBODY
L: ANTI-VEGF-B MONOCLONAL ANTIBODY


Theoretical massNumber of molelcules
Total (without water)132,3556
Polymers132,3556
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16980 Å2
ΔGint-119.7 kcal/mol
Surface area58540 Å2
MethodPQS
Unit cell
Length a, b, c (Å)86.200, 94.300, 91.300
Angle α, β, γ (deg.)90.00, 102.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein VASCULAR ENDOTHELIAL GROWTH FACTOR B / VEGF-B / VEGF-RELATED FACTOR / VRF / VASCULAR ENDOTHELIAL GROWTH FACTOR-B


Mass: 19053.236 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15PREP4 / References: UniProt: P49765
#2: Antibody ANTI-VEGF-B MONOCLONAL ANTIBODY


Mass: 23633.018 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse)
#3: Antibody ANTI-VEGF-B MONOCLONAL ANTIBODY


Mass: 23491.373 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.1 % / Description: NONE
Crystal growpH: 7 / Details: 0.1 M HEPES PH 7.0 15% GLYCEROL 8% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 25, 2005 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.4→3.61 Å / Num. obs: 17540 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 47.8 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.4
Reflection shellResolution: 3.4→3.6 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.7 / % possible all: 72.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CFN AND 2C7W

1cfn

2c7w


Resolution: 3.4→19.78 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. BULK SOLVENT MODEL USED RESIDUES FOR WHICH NO DENSITY WAS OBSERVED BEYOND C-BETA WERE MODELLED AS ALANINES OR GLYCINES
RfactorNum. reflection% reflectionSelection details
Rfree0.31 1325 7.9 %RANDOM
Rwork0.262 ---
obs0.286 16684 88.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT MODEL
Displacement parametersBiso mean: 53.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.4→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8109 0 0 0 8109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228310
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.41.95311324
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.4→3.61 Å / Total num. of bins used: 6 /
RfactorNum. reflection
Rfree0.415 158
Rwork0.371 1439

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